To alleviate the problems in the receptor-based design of metalloprotein ligands due to inadequacies in the force-field description of coordination bonds, a four-tier approach was devised. Representative ligand-metalloprotein interaction energies are obtained by subsequent application of (1) docking with metal-binding-guided selection of modes; (2) optimization of the ligand-metalloprotein complex geometry by combined quantum mechanics and molecular mechanics (QM/MM) methods; (3) conformational sampling of the complex with constrained metal bonds by force-field based molecular dynamics (MD); and (4) a single point QM/MM energy calculation for the time-averaged structures. The QM/MM interaction energies are, in a linear combination with the desolvation-characterizing changes in the solvent-accessible surface areas, correlated with experimental data. The approach was applied to structural correlation of published binding free energies of a diverse set of 28 hydroxamate inhibitors to zinc-dependent matrix metalloproteinase 9 (MMP-9). Inclusion of step 3 and step 4 significantly improved both correlation and prediction. The two descriptors explained 90% of variance in inhibition constants of all 28 inhibitors, ranging from 0.08 to 349 nM, with the average unassigned error of 0.318 log units. The structural and energetic information obtained from the timeaveraged MD simulation results helped understand the differences in binding modes of related compounds.

The currently recommended doses of rifampin are believed to be at the lower end of the dose-response curve. Rifampin induces its own metabolism, although the effect of dose on the extent of autoinduction is not known. This study aimed to investigate rifampin autoinduction using a semimechanistic pharmacokinetic-enzyme turnover model. Four different structural basic models were explored to assess whether different scaling methods affected the final covariate selection procedure. Covariates were selected by using a linearized approach. The final model included the allometric scaling of oral clearance and apparent volume of distribution. Although HIV infection was associated with a 30% increase in the apparent volume of distribution, simulations demonstrated that the effect of HIV on rifampin exposure was slight. Model-based simulations showed close-to-maximum induction achieved after 450-mg daily dosing, since negligible increases in oral clearance were observed following the 600-mg/day regimen. Thus, dosing above 600 mg/day is unlikely to result in higher magnitudes of autoinduction. In a typical 55-kg male without HIV infection, the oral clearance, which was 7.76 liters · h ؊1 at the first dose, increased 1.82-and 1.85-fold at steady state after daily dosing with 450 and 600 mg, respectively. Corresponding reductions of 41 and 42%, respectively, in the area under the concentration-versus-time curve from 0 to 24 h were estimated. The turnover of the inducible process was estimated to have a half-life of approximately 8 days in a typical patient. Assuming 5 half-lives to steady state, this corresponds to a duration of approximately 40 days to reach the induced state for rifampin autoinduction. Rifampin is an indispensable constituent of first-line therapy used to treat drug-susceptible Mycobacterium tuberculosis. During the 2-month intensive phase of standard short-course antituberculosis treatment, patients receive rifampin together with isoniazid, pyrazinamide, and ethambutol. Rifampin and isoniazid are given for a further 4-month continuation phase, completing the 6-month treatment regimen. Isoniazid is responsible for killing the majority of organisms within the first 2 days of treatment. From the third to the seventh day of treatment, rifampin and pyrazinamide continue the bactericidal function (30), while ethambutol protects against the development of rifampin resistance in the event of preexisting isoniazid resistance (8). The ability of rifampin to eradicate persisting organisms has allowed the shortening of treatment from 12 to 6 months (43).Rifampin is a potent activator of the nuclear pregnane X receptor (PXR), which regulates the transcription of multiple drugmetabolizing enzymes and drug transporters (9, 13). Although the exact mechanism is not known, following chronic intravenous or oral dosing, rifampin induces its own metabolism by increasing its systemic and presystemic clearances (27,31). This effect might, in part, be attributed to the PXR-mediated induction of P-glycoprotein (P-gp), a trans-mem...

Organic anion transporters (OATs, SLC22) interact with a remarkably diverse array of endogenous and exogenous organic anions. However, little is known about the structural features that determine their substrate selectivity. We examined the substrate binding preferences and transport function of olfactory organic anion transporter, Oat6, in comparison with the more broadly expressed transporter, Oat1 (first identified as NKT). In analyzing interactions of both transporters with over 40 structurally diverse organic anions, we find a correlation between organic anion potency (pK i ) and hydrophobicity (logP) suggesting a hydrophobicity-driven association with transporter-binding sites, which appears particularly prominent for Oat6. On the other hand, organic anion binding selectivity between Oat6 and Oat1 is influenced by the anion mass and net charge. Smaller mono-anions manifest greater potency for Oat6 and di-anions for Oat1. Comparative molecular field analysis confirms these mechanistic insights and provides a model for predicting new OAT substrates. By comparative molecular field analysis, both hydrophobic and charged interactions contribute to Oat1 binding, although it is predominantly the former that contributes to Oat6 binding. Together, the data suggest that, although the three-dimensional structures of these two transporters may be very similar, the binding pockets exhibit crucial differences. Furthermore, for six radiolabeled substrates, we assessed transport efficacy (V max ) for Oat6 and Oat1. Binding potency and transport efficacy had little correlation, suggesting that different molecular interactions are involved in substrate binding to the transporter and translocation across the membrane. Substrate specificity for a particular transporter may enable design of drugs for targeting to specific tissues (e.g. olfactory mucosa). We also discuss how these data suggest a possible mechanism for remote sensing between OATs in different tissue compartments (e.g. kidney, olfactory mucosa) via organic anions.

Avelumab, a human anti–programmed death ligand 1 immunoglobulin G1 antibody, has shown efficacy and manageable safety in multiple tumors. A two‐compartment population pharmacokinetic model for avelumab incorporating intrinsic and extrinsic covariates and time‐varying clearance ( CL ) was identified based on data from 1,827 patients across three clinical studies. Of 14 tumor types, a decrease in CL over time was more notable in metastatic Merkel cell carcinoma and squamous cell carcinoma of the head and neck, which had maximum decreases of 32.1% and 24.7%, respectively. The magnitude of reduction in CL was higher in responders than in nonresponders. Significant covariate effects of baseline weight, baseline albumin, and sex were identified on both CL and central distribution volume. Significant covariate effects of black/African American race, C‐reactive protein, and immunogenicity were found on CL . None of the covariate or time‐dependent effects were clinically important or warranted dose adjustment.

The pregnane X receptor (PXR) regulates the expression of genes involved in xenobiotic metabolism and transport. In vitro methods to screen for PXR agonists are used widely. In the current study, computational models for human PXR activators and PXR nonactivators were developed using recursive partitioning (RP), random forest (RF), and support vector machine (SVM) algorithms with VolSurf descriptors. Following 10-fold randomization, the models correctly predicted 82.6-98.9% of activators and 62.0-88.6% of nonactivators. The models were validated using separate test sets. The overall ( n = 15) test set prediction accuracy for PXR activators with RP, RF, and SVM PXR models is 80-93.3%, representing an improvement over models previously reported. All models were tested with a second test set ( n = 145), and the prediction accuracy ranged from 63 to 67% overall. These test set molecules were found to cover the same area in a principal component analysis plot as the training set, suggesting that the predictions were within the applicability domain. The FlexX docking method combined with logistic regression performed poorly in classifying this PXR test set as compared with RP, RF, and SVM but may be useful for qualitative interpretion of interactions within the LBD. From this analysis, VolSurf descriptors and machine learning methods had good classification accuracy and made reliable predictions within the model applicability domain. These methods could be used for high throughput virtual screening to assess for PXR activation, prior to in vitro testing to predict potential drug-drug interactions.

Long-term exposure to antivirals is associated with serious cellular toxicity to the kidney and other tissues. Organic anion transporters (OATs) are believed to mediate the cellular uptake, and hence cytotoxicity, of many antivirals. However, a systematic in vitro and ex vivo analysis of interactions between these compounds with various OAT isoforms has been lacking. To characterize substrate interactions with mOat1, mOat3, and mOat6, a fluorescence-based competition assay in Xenopus oocytes as well as wild-type and knock-out whole embryonic kidney (WEK) organ culture systems was developed using 6-carboxyfluorescein, 5-carboxyfluorescein, and fluorescein. Of nine common antiviral drugs assessed in oocytes, many manifested higher affinity for SLC22a6 (mOat1), originally identified as NKT (e.g. adefovir and cidofovir), two (ddC and ddI) manifested significantly higher affinity for mOat3, while mOat6 had comparatively low but measurable affinity for certain antivirals. A live organ staining approach combined with fluorescent uptake in WEK cultures allowed the visualization of OAT-mediated uptake ex vivo into developing proximal tubule-like structures, as well as quantification of substrate interactions of individual OAT isoforms. In general, antiviral specificity of SLC22a6 (Oat1) (in Oat3 ؊/؊ WEK culture) and SLC22a8 (Oat3) (in Oat1 ؊/؊ WEK culture) was consistent with the Xenopus oocyte data. The combined observations suggest SLC22a8 (Oat3) is the major transporter interacting with ddC and ddI. Finally, quantitative structure-activity relationship analysis of the nine antivirals' physicochemical descriptors with their OAT affinity indicates that antiviral preferences of mOat1 are explained by high polar surface areas (e.g. phosphate groups), whereas mOat3 prefers hydrogen bond acceptors (e.g. amines, ketones) and low rotatable bond numbers. In contrast, hydrogen bond donors (e.g. amides, alcohols) diminish binding to mOat6. This suggests that, despite sharing close overall sequence homology, Oat1, Oat3, and Oat6 have signficantly different binding pockets. Taken together, the data provide a basis for understanding potential drug interactions in combination antiviral therapy, as well as suggesting structural mdifications for drug design, especially in the context of targeting toward or away from specific tissues.The organic anion transporters (OATs) 2 mediate the uptake of structurally diverse substrates: endogenous compounds (steroids, odorants, cyclic nucleotides, neurotransmitters), drugs (non-steroidal anti-inflammatory drugs, diuretics, and antibiotics), environmental toxins (ochratoxin A and mercuric chlorides), and other organic wastes (1, 2). It has recently been hypothesized that OATs and other SLC22 family members participate in a remote sensing mechanism for small molecules between tissues and also between organisms (1, 23). The prototype, now called Oat1, was initially identified as NKT (3-5). Since then, at least six OATs have been identified, all of which are members of the larger SLC22 family of tra...

Background M5717 is the first plasmodium translation elongation factor 2 inhibitor to reach clinical development as an antimalarial. We aimed to characterise the safety, pharmacokinetics, and antimalarial activity of M5717 in healthy volunteers. MethodsThis first-in-human study was a two-part, single-centre clinical trial done in Brisbane, QLD, Australia. Part one was a double-blind, randomised, placebo-controlled, single ascending dose study in which participants were enrolled into one of nine dose cohorts (50, 100, 200, 400, 600, 1000, 1250, 1800, or 2100 mg) and randomly assigned (3:1) to M5717 or placebo. A sentinel dosing strategy was used for each dose cohort whereby two participants (one assigned to M5717 and one assigned to placebo) were initially randomised and dosed. Randomisation schedules were generated electronically by independent, unblinded statisticians. Part two was an open-label, nonrandomised volunteer infection study using the Plasmodium falciparum induced blood-stage malaria model in which participants were enrolled into three dose cohorts. Healthy men and women of non-childbearing potential aged 18-55 years were eligible for inclusion; individuals in the volunteer infection study were required to be malaria naive. Safety and tolerability (primary outcome of the single ascending dose study and secondary outcome of the volunteer infection study) were assessed by frequency and severity of adverse events. The pharmacokinetic profile of M5717 was also characterised (primary outcome of the volunteer infection study and secondary outcome of the single ascending dose study). Parasite clearance kinetics (primary outcome of the volunteer infection study) were assessed by the parasite reduction ratio and the corresponding parasite clearance half-life; the incidence of recrudescence up to day 28 was determined (secondary outcome of the volunteer infection study). Recrudescent parasites were tested for genetic mutations (exploratory outcome). The trial is registered with ClinicalTrials.gov (NCT03261401).

Avelumab, an anti–programmed death‐ligand 1 monoclonal antibody approved for the treatment of metastatic Merkel cell carcinoma and platinum‐treated urothelial carcinoma, was initially approved with a 10 mg/kg weight‐based dose. We report pharmacokinetic (PK)/pharmacodynamic analyses for avelumab comparing weight‐based dosing and a flat 800 mg dose, developed using data from 1,827 patients enrolled in 3 clinical trials (NCT01772004, NCT01943461, and NCT02155647). PK metrics were simulated for weight‐based and flat‐dosing regimens and summarized by quartiles of weight. Derived exposure metrics were used in simulations of exposure‐safety (various tumors) and exposure‐efficacy (objective responses; Merkel cell or urothelial carcinoma). Flat dosing was predicted to provide similar exposure to weight‐based dosing, with slightly lower variability. Exposure‐safety and exposure‐efficacy simulations suggested similar benefit:risk profiles for the two dosing regimens. These pharmacometric analyses provided the basis for the US Food and Drug Administration approval of a flat dose of avelumab 800 mg every 2 weeks in approved indications.